Familial clustering of autoimmune disease is well recognised and raises the possibility that some susceptibility genes may predispose to autoimmunity in general. In light of this observation it might be expected that some of the variants of established relevance in one autoimmune disease may also be relevant in other related conditions. Based on this hypothesis we tested seven single nucleotide polymorphisms (SNPs) that are known to be associated with type 1 diabetes in a large multiple sclerosis dataset consisting of 2,369 trio families, 5,737 cases and 10,296 unrelated controls. Two of these seven SNPs demonstrated evidence for association with multiple sclerosis; rs12708716 from the CLEC16A gene (p= 1.6× 10− 16) and rs763361 from the CD226 gene (p= 5.4× 10− 8). These findings thereby identify two additional multiple sclerosis susceptibility genes and lend support to the notion of autoimmune susceptibility genes.